Rifabutin treatment methods, uses and compositions

Abstract

Systems and methods for increasing the clinical efficacy of rifabutin against A. baumannii are provided.SOLUTION: The present invention takes advantage of the discovery of the ferric-coprogen (FhuE) receptor responsible for the uptake of rifabutin into A. baumannii cells. Preferably, a method includes obtaining a sample from a patient suspected of having an infection; performing a test on the sample to identify an A. baumannii infection in the patient; and providing a formulation of rifabutin for treating the patient that maximizes the resulting AUC and / or Cmax when administered to the patient. The method may comprise administering a formulation of rifabutin to the patient. Preferably, the formulation is delivered to the patient such as by intravenous infusion and results in a Cmax that is greater than about 2mg / L and optionally less than about 50mg / L.SELECTED DRAWING: None

Description

[Technical Field]

[0001] Related Applications This application claims the benefit of and priority to U.S. Provisional Patent Application Nos. 62 / 902,019, filed September 18, 2019, 62 / 899,257, filed September 12, 2019, 62 / 941,160, filed November 27, 2019, and 62 / 977,659, filed February 17, 2020, the contents of each of which are incorporated herein by reference in their entirety.

[0002] Technical Field The present invention provides compositions and methods for activation of the A. baumannii ferric iron-coprogen (FhuE) receptor and methods for achieving high systemic exposure (C) of rifabutin effective for treating A. baumannii infection. max and AUC). [Background technology]

[0003] background Bacterial infections are often difficult to treat due to the emergence of multidrug-resistant (MDR) or extensively drug-resistant (XDR) bacterial strains. Of particular concern are carbapenem- and third-generation cephalosporin-resistant Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacteriaceae spp., which, according to the World Health Organization's priority list, belong to the antimicrobial-resistant Gram-negative pathogens known by the acronym "ESKAPE."

[0004] Because patients suffering from antimicrobial-resistant infections are usually too ill to take oral formulations of "last resort" antibiotics, intravenous (IV) administration is the only satisfactory delivery method for providing antibiotic treatment. Unfortunately, most antibiotics are not formulated for IV administration because they are difficult or impossible to formulate into a soluble form.

[0005] Rifabutin (also known as LM427 and Mycobutin®) is a spiro-piperidyl-rifamycin derived from rifamycin-S. Mycobutin® was approved by the FDA as an oral formulation in 1992. Mycobutin® (150 mg capsules) capsules are prescribed for the prevention of disseminated Mycobacterium avium complex (MAC) disease in patients with advanced HIV infection. Rifabutin is widely known to have low outer membrane permeability to Gram-negative pathogens, thereby limiting its cellular uptake into these life-threatening ESKAPE pathogens. Thus, formulations or alternative routes of administration for rifabutin have not been fully explored, a situation exacerbated by its poor solubility.

[0006] For closely related rifamycin molecules (e.g., rifampin (also known as rifampicin)), microbial kill of Mycobacterium tuberculosis is related to the area under the concentration-time curve versus MIC ratio (AUC / MIC), whereas suppression of resistance is related to the free peak concentration (C max )-to-MIC ratio (C max / MIC) and was not related to the duration of rifampin concentrations above the MIC. Furthermore, postantibiotic duration of effect was also related to C max / MIC ratio (Gumbo, 2007, Concentration-dependent Mycobacterium tuberculosis killing and prevention of resistance by rifampin, Antimicrobial Agents and Chemotherapy, 51(11):3781-3788 (incorporated by reference). Thus, high plasma drug concentrations are required to achieve microbial kill and prevent the emergence of resistance in the clinical setting.

[0007] In healthy adult volunteers, a nominal therapeutic oral dose of 300 mg rifabutin resulted in a mean C of 0.375 mg / L, achieved approximately 3 hours after oral administration. max (Rifabutin Product Monograph). The PK of rifabutin has been shown to produce C values ​​ranging from 0.4 to 0.7 mg / L after single doses of 300 mg, 450 mg, and 600 mg PO to healthy volunteers. max (Rifabutin product monograph). In studies in HIV-infected patients receiving the recommended daily dose of rifabutin (300 mg / day), steady-state plasma concentrations were max The mean RI concentration was 0.59±0.33 mg / L, and the AUC was 8.6±8.2 mg*h / L (Hafner, 1998, Tolerance and pharmacokinetic interactions of rifabutin and clarithromycin in human immunodeficiency virus-infected volunteers, Antimicrobial Agents and Chemotherapy 42(3):631-639 (incorporated by reference).

[0008] Rifabutin is approximately 90% protein-bound, resulting in very low free drug concentrations after oral administration. In healthy adult volunteers, at least 53% of an oral dose is absorbed, whereas absolute bioavailability assessed in HIV-positive patients was 20% on day 1 and 12% on day 28 in a multiple-dose study. The low systemic exposure (C) of rifabutin after oral administration max The RI and AUC (Analysis of RI and AUC) limit the usefulness of rifabutin for the treatment of serious infections such as those caused by the ESKAPE pathogen Acinetobacter baumannii (Acinetobacter calcoaceticus-baumannii complex). Furthermore, oral administration of rifabutin to patients with such infections is likely to result in the rapid development of resistance. [Prior art documents] [Non-patent literature]

[0009] [Non-Patent Document 1] Gumbo, 2007, Concentration-dependent Mycobacterium tuberculosis killing and prevention of resistance by rifampin, Antimicrobial Agents and Chemotherapy, 51(11):3781-3788 [Non-patent document 2] Hafner, 1998, Tolerance and pharmacokinetic interactions of rifabutin and clarithromycin in human immunodeficiency virus-infected volunteers, Antimicrobial Agents and Chemotherapy 42(3):631-639 Summary of the Invention [Means for solving the problem]

[0010] Abstract The present invention provides systems and methods for increasing the clinical effectiveness of rifabutin against A. baumannii. The inventors' discovery of a novel mechanism of action has resulted in the ability of rifabutin to maintain significant activity against A. baumannii while having only minimal activity against other Gram-negative pathogens. The present invention utilizes the discovery of the ferric iron-coprogen (FhuE) receptor, which is responsible for the uptake of rifabutin (but not the closely related drug, rifampin) into A. baumannii cells. In one aspect, the present invention provides high AUC and C of administered rifabutin. maxThis provides a compound that allows for increased clinical efficacy through activation of the FhuE receptor, while simultaneously reducing the potential for resistance - a significant problem with standard oral formulations of rifabutin and related drugs. max However, localized high C max and AUC, when required, can be achieved by intravenous injection, or by methods known in the art for modified oral release, or by inhalation.

[0011] In certain embodiments, a rifabutin liquid formulation is provided for intravenous (IV) administration, and the formulation is effective against Acinetobacter baumannii. The rifabutin liquid formulation may utilize a siderophore that modulates the ferric iron-coprogen (FhuE) receptor in the bacterial cell membrane to transport rifabutin across the bacterial cell membrane. This provides a previously unknown and unexpected clinical advantage for oral rifabutin. The rifabutin formulations disclosed herein are useful for treating bacterial infections where oral administration of antimicrobial agents is impractical or impossible. The formulations and methods of the present invention offer the medical industry a novel treatment for patients incapacitated by life-threatening bacterial infections.

[0012] In certain embodiments, rifabutin utilizes the presence of a siderophore that regulates a TonB-dependent siderophore receptor in bacterial cells. The TonB-dependent siderophore receptor may be the ferric-coprogen (FhuE) receptor. A preferred siderophore is one that regulates a bacterial TonB-dependent siderophore receptor. For example, a preferred siderophore may be any iron chelator that mediates the uptake of rifabutin into the TonB-dependent siderophore receptor. For example, the siderophore may be apotransferrin or transferrin. The siderophore may be loaded with an iron complex. The iron-loaded siderophore may be transferrin.

[0013] Rifabutin may utilize the presence of siderophores that modulate the TonB-dependent siderophore receptors of Acinetobacter baumannii.

[0014] As noted, the methods of the present invention demonstrate that FhuE receptor activation allows rifabutin to enter A. baumannii and further enhances the high C maxThis is based on the recognition that a RIFABUTIN concentration of approximately 25% to approximately 75%, approximately 30% to approximately 70%, approximately 35% to approximately 65%, approximately 40% to approximately 60%, approximately 45% to approximately 55%, approximately 45% to approximately 65%, approximately 50% to approximately 65%, approximately 50% to approximately 60%, approximately 50% to approximately 55%, or approximately 50%. Preferably, the RIFABUTIN concentration and distilled water are in a 1:1 ratio. Preferred solvents include polyoxyethylene sorbitan monooleate (Tween® 80), polyoxyethylene sorbitan monolaurate (Tween® 20), polyethylene glycol (PEG), propylene glycol, N-methyl-2-pyrrolidone (NMP), glycerin, ethanol, dimethylacetamide (DMA), diethylene glycol monoethyl ether (Transcutol HP), or dimethyl isosorbide (DMI). In a preferred embodiment, the solvent is DMI. Reconstituted solutions of the present invention preferably contain about 250 mg / ml (1:1 solvent / water) or about 166.7 mg / ml (2:1 solvent / water), although the concentration of the reconstituted solution can be as high as about 300 mg / ml. In certain embodiments, a more dilute solution is required, which can be achieved by adding more water to the solvent. For example, rifabutin at a 1:4 solvent / water ratio produces a solution of about 50 mg / ml. Such formulations are useful for treating a variety of conditions caused by A. baumannii, including, but not limited to, bacteremia, ventilator-associated bacterial pneumonia (VABP), hospital-acquired bacterial pneumonia (HABP), and urinary tract infections (UTIs).

[0015] According to the present invention, rifabutin has potent activity against A. baumannii due to utilization of the A. baumannii ferric iron-coprogen (FhuE) receptor. Additionally, the present invention provides a method for determining the susceptibility of A. baumannii isolates to rifabutin treatment.

[0016] In accordance with the present invention, the disclosed intravenous formulations provide significant C[upsilon][iota ... max and AUC. This provides an unexpected clinical advantage not previously available for rifabutin. Intravenous administration of rifabutin provides a novel treatment for patients with life-threatening bacterial infections (e.g., those caused by Acinetobacter baumannii).

[0017] The formulations of the present invention contain an acid. The solvent solution may also contain an acid. The acid may be added to the solvent solution to form a reconstitution solvent. The acid may be at a concentration sufficient to cause dissolution of rifabutin when added to the reconstitution solvent. The acid may be present in a concentration of about 1.0% to about 5.0%, about 1.1% to about 4.9%, about 1.2% to about 4.8%, about 1.3% to about 4.7%, about 1.4% to about 4.6%, about 1.5% to about 4.5%, about 1.6% to about 4.4%, about 1.7% to about 4.3%, about 1.8% to about 4.2%, about 1.9% to about 4.1%, about 2.0% to about 4.0%, about 2.1% to about 3.9%, or about 2.2% to about 3. The acid concentration may be about 8%, about 2.3% to about 3.7%, about 2.4% to about 3.6%, about 2.5% to about 3.5%, about 2.5% to about 3.4%, about 2.5% to about 3.3%, about 2.5% to about 3.2%, about 2.5% to about 3.1%, about 2.5% to about 3.0%, about 2.5% to about 2.9%, about 2.5% to about 2.8%, about 2.5% to about 2.7%, or about 2.5% to about 2.6%. The acid may be hydrochloric acid, methanesulfonic acid, phosphoric acid, l-tartaric acid, d-glucuronic acid, l-malic acid, d-gluconic acid, l-lactic acid, acetic acid, or l-aspartic acid. Preferably, the acid is acetic acid.

[0018] The acid-containing formulations have a pH of about 3.0 to about 10.0, about 3.0 to about 9.0, about 3.0 to about 8.0, about 3.0 to about 7.0, about 3.0 to about 6.0, about 4.0 to about 10.0, about 4.0 to about 9.0, about 4.0 to about 8.0, about 4.0 to about 7.0, about 4.0 to about 6.0, about 5.0 to about 6.0, about 5.1 to about 5.9, about 5.2 to about 5.8, about 5.3 to about 5.7, about 5.4 to about 5.6, about 5.5 to about 5.6, about 5.5 to about 5.7, about 5.5 to about 5.8, about 5.5 to about 5.9, or a pH of >4.5. Preferably, the pH is about 5.0 to about 6.0.

[0019] Intravenous rifabutin formulations can be manufactured by a process that includes preparing a solution containing a solvent and distilled water in a 1:1 ratio in the presence of an acid suitable for promoting the dissolution of rifabutin. Rifabutin can be in a solid form or in a powder form that is soluble in a liquid medium. Rifabutin can be dissolved in a solvent. Rifabutin can be soluble in an aqueous solution of 50% solvent (i.e., 1:1 solvent-distilled water) in the presence of an acid.

[0020] Thus, rifabutin can be dissolved in a reconstitution solution comprising an acid in an aqueous solution of a solvent in distilled water. Rifabutin can be added to the reconstitution solvent in an amount sufficient to produce a final solution having rifabutin at a concentration of about 150 mg / mL to about 350 mg / mL, about 160 mg / mL to about 325 mg / mL, about 170 mg / mL to about 300 mg / mL, about 180 mg / mL to about 275 mg / mL, about 190 mg / mL to about 265 mg / mL, about 200 mg / mL to about 255 mg / mL, about 210 mg / mL to about 250 mg / mL, about 225 mg / mL to about 255 mg / mL, about 235 mg / mL to about 255 mg / mL, about 245 mg / mL to about 255 mg / mL, or about 250 mg / mL to about 255 mg / mL. Preferably, the rifabutin solution or salt thereof contains about 250 mg / mL rifabutin. Adding the rifabutin to the reconstituted solution forms a reconstituted solution of rifabutin. The reconstituted rifabutin solution or salt thereof may be a concentrated solution that is not yet ready for parenteral administration. The concentrated solution may be a sterile solution.

[0021] The rifabutin solution of the present invention can be in the form of a formulation for parenteral administration.The reconstituted rifabutin solution can be diluted with a pharmaceutically acceptable diluent for intravenous administration of a therapeutically effective dose of rifabutin.For example, the reconstituted rifabutin solution can be added to a pharmaceutically acceptable diluent to prepare it for sterile injection into a subject.The diluent can be sodium chloride solution.

[0022] The formulation may include a solvent. In various embodiments, the w / v ratio of rifabutin to solvent may be about 4:1 to about 1:4, about 2:1 to about 1:3, or about 1:1 to about 1:2. The w / v ratio of rifabutin to solvent may be about 4:1, about 3:1, about 2:1, about 1:1, about 1:2, about 1:3, or about 1:4.

[0023] In certain embodiments, the formulations may be provided to achieve a systemic concentration of rifabutin of about 2 mg / L to about 50.0 mg / L.

[0024] The formulations of the present invention may be for any parenteral administration. For example, the compositions may be formulated for injection, infusion, or inhalation. The injection may be subcutaneous or intravenous. Preferably, the compositions are formulated for intravenous administration. Thus, the formulations of the present invention may also contain a pharmaceutically acceptable diluent. The pharmaceutically acceptable diluent may be at a concentration sufficient to deliver a therapeutically effective amount of rifabutin in an IV formulation to a patient suffering from an infectious disease. The pharmaceutically acceptable diluent may be saline. Preferably, the diluent is 0.9% saline. The solution may be administered with a therapeutically effective amount of rifabutin to treat a patient suffering from an infectious disease.

[0025] In certain aspects, the present disclosure provides a method for treating A. baumannii infection. The method comprises administering to a patient a composition comprising rifabutin at a dose sufficient to activate the ferric iron-coprogen (FhuE) receptor of the A. baumannii cells, thereby promoting the entry of the rifabutin into the A. baumannii cells. Preferably, the composition is administered intravenously. The dose is selected from the group consisting of AUC and C associated with FhuE receptor activation. max , e.g., preferably greater than about 2 mg / L max The above C can be provided. max may be greater than about 2 mg / L and less than about 50 mg / L. max Rifabutin may be administered with a rifabutin concentration >2 mg / L but <50 mg / L and an AUC >10 mg*h / L and <300 mg*h / L.

[0026] In a preferred embodiment, the composition comprises rifabutin, water, a solvent, and an acid. The composition is administered intravenously at a rifabutin dosage of at least about 2 mg / kg q24h, 1 mg / kg q12h, or 0.5 mg / kg q6h. The solvent can be, for example, polyoxyethylene sorbitan monooleate (Tween® 80), polyoxyethylene sorbitan monolaurate (Tween® 20), polyethylene glycol (PEG), propylene glycol, N-methyl-2-pyrrolidone (NMP), glycerin, ethanol, dimethylacetamide (DMA), diethylene glycol monoethyl ether (transcutol HP), or dimethyl isosorbide (DMI). The composition can have a v / w solvent:rifabutin of about 2:1. The method preferably comprises delivering the formulation to the patient at a dosage that results in a C max of at least about 2 mg / L. max The formulation can be delivered at a dosage that results in 2 mg / L < C

[0027] An aspect of the present disclosure provides a composition for use in treating A. baumannii infection, the composition comprising rifabutin, water, a solvent, and an acid. The composition is an aqueous solution with a high concentration of rifabutin (e.g., 2:1 v / w solvent:rifabutin) that promotes rifabutin entry into A. baumannii cells by activating the ferric-coprogen (FhuE) receptor on the cells. The solvent can be, for example, polyoxyethylene sorbitan monooleate (Tween® 80), polyoxyethylene sorbitan monolaurate (Tween® 20), polyethylene glycol (PEG), propylene glycol, N-methyl-2-pyrrolidone (NMP), glycerin, ethanol, dimethylacetamide (DMA), diethylene glycol monoethyl ether (transcutol HP), or dimethyl isosorbide (DMI). In a preferred embodiment, the solvent is DMI or transcutol HP.

[0028] In certain embodiments, the v / v ratio of the solvent to water is 1:1 or 1:2. The acid can be hydrochloric acid, methanesulfonic acid, phosphoric acid, L-tartaric acid, D-glucuronic acid, L-malic acid, D-gluconic acid, L-lactic acid, acetic acid, or L-aspartic acid. In a preferred embodiment, the acid is acetic acid or D-glucuronic acid. In certain embodiments, the molar ratio of rifabutin to acid is 1:1.

[0029] Preferably, the composition is provided as an aqueous solution for intravenous delivery. The composition may be provided for a patient identified as infected with A. baumannii, and may comprise rifabutin for IV delivery at a dosage of at least about 2 mg / kg q24h, 1 mg / kg q12h, or 0.5 mg / kg q6h.

[0030] In a related aspect, the present disclosure provides the use of rifabutin for the manufacture of a medicament for treating A. baumannii infection in a patient. The medicament may provide a dose that results in an AUC and C related to activation of the FhuE receptor. max Preferably, the medicament is prepared to be administered at a dosing regimen that results in a C of at least about 2 mg / L in the patient. max The medicament may comprise rifabutin, water, a solvent, and an acid. The solvent may be, for example, polyoxyethylene sorbitan monooleate (Tween® 80), polyoxyethylene sorbitan monolaurate (Tween® 20), polyethylene glycol (PEG), propylene glycol, N-methyl-2-pyrrolidone (NMP), glycerin, ethanol, dimethylacetamide (DMA), diethylene glycol monoethyl ether (transcutol HP), or dimethyl isosorbide (DMI). The medicament may be provided within an IV bag. Preferably, the medicament provides a dose that results in 2 mg / L < C max < 50 mg / L; and 10 mg*h / L < AUC < 300 mg*h / L. In certain embodiments, the medicament provides a rifabutin dosage that is at least about 2 mg / kg q24h, 1 mg / kg q12h, or 0.5 mg / kg q6h.

[0031] In another aspect, the present invention provides a method for preparing an intravenous formulation of rifabutin. The method may include the step of preparing a solution comprising a solvent and distilled water. Preferably, the solution is in a 1:1 ratio. The solvent may be any solvent, but is preferably DMI. An acid may be added to the solution. The acid may be suitable for promoting the dissolution of rifabutin. The acid may be any acid, but is preferably acetic acid. Rifabutin may be introduced into the solution containing the acid. Thus, the acid causes rifabutin to dissolve into the solution.

[0032] The rifabutin solution may be added to a pharmaceutically acceptable diluent. The diluent may be 0.9% saline. An intravenous formulation of rifabutin may contain rifabutin, DMI, and saline. The w / v ratio of rifabutin to solvent may be about 4:1 to about 1:4, about 2:1 to about 1:3, or about 1:1 to about 1:2. The w / v ratio of rifabutin to solvent may be about 4:1, about 3:1, about 2:1, about 1:1, about 1:2, about 1:3, or about 1:4. The amounts and concentrations of rifabutin, DMI, and saline will depend on the size of the IV bag (in intravenous embodiments); such variations, along with the amount of DMI determined based on the above ratio, will be apparent to those skilled in the art to achieve a preferred dose in the range of 6 to 9 mg / kg. An intravenous formulation of rifabutin may be administered to a subject in need of treatment.

[0033] In another aspect, the present invention provides a method for increasing the effectiveness of an antibiotic. The method includes modulating a TonB-dependent siderophore receptor in a bacterial cell to increase antibiotic uptake. Modulating the TonB-dependent siderophore receptor can include administering an IV formulation of the antibiotic, which mediates transport of the antibiotic across the bacterial cell membrane. The TonB-dependent siderophore receptor can be an FhuE receptor. Administering an IV formulation of the antibiotic increases the antibiotic's bioavailability, thereby increasing its uptake across the bacterial cell membrane. The antibiotic can be any form of rifabutin that can be administered IV. The siderophore can be bound to an iron complex. Rifabutin can bind to an iron-loaded siderophore or cross the cell membrane using the TonB-dependent siderophore receptor mediation of the iron-loaded siderophore. The IV formulation can be of any IV formulation of rifabutin or its doses described herein.

[0034] In another aspect, the present invention provides a method for treating a bacterial infection. The method may include administering a liquid formulation of rifabutin to a subject with a bacterial infection. The liquid formulation may include rifabutin or a salt thereof, a solvent, and an acid. The liquid formulation may be a solution of rifabutin and a diluent to be administered intravenously to a subject with a bacterial infection. The rifabutin can then translocate across the outer membrane of the infecting bacterial cells and eradicate the bacterial cells. The bacterial infection may be any infection caused by A. baumannii, including, but not limited to, bacteremia, ventilator-associated bacterial pneumonia (VABP), hospital-acquired bacterial pneumonia (HABP), and urinary tract infections (UTIs). A formulation for IV administration may include a pharmaceutically acceptable solvent. The method may include administering an IV formulation of any of the formulations of rifabutin described herein to a subject suffering from a bacterial infection.

[0035] Without being bound by theory, any formulation of the present invention may be used in any of the methods of the present invention.

[0036] In another aspect, the method of the present invention can include identifying a compound having antibacterial activity against Acinetobacter baumannii. The method can include providing a medium containing at least an iron complex and an iron chelator, introducing a plurality of A. baumannii bacterial cells into the medium, and exposing the medium containing the plurality of bacterial cells to a compound. The method can also include quantifying the plurality of bacterial cells using any acceptable method for bacterial quantification. Identifying a reduction in the number of the plurality of bacterial cells indicates antibacterial activity of the compound.

[0037] The reduction in the number of bacterial cells can occur when the compound disrupts the bacterial cells by crossing their outer membrane. The compound can cross the outer membrane in the presence of an iron complex or iron chelator, thus enabling Ton-B siderophore receptor-mediated uptake of the compound. The receptor can be the FhuE receptor.

[0038] The medium may be Roswell Park Memorial Institute (RPMI) medium, 10% fetal bovine serum, or a combination thereof. The medium may be any medium, or any medium that either contains iron and an iron chelator or may have iron and an iron chelator added to the medium. The iron complex may be any iron complex capable of binding to a siderophore. The iron chelator may be any iron chelator capable of crossing the bacterial cell membrane. Preferably, the iron chelator is pyridoxal isonicotinoyl hydrazone (PIH). The chelator may be present at a concentration of about 0.05 mM to 0.25 mM, about 0.075 mM to 0.225 mM, about 0.1 mM to 0.2 mM, or about 0.125 mM to 0.15 mM. Preferably, the iron chelator is present at about 0.1 mM.

[0039] In another aspect of the present invention, a method includes treating a bacterial infection in a subject. The method may include administering a therapeutically effective amount of an intravenous formulation of rifabutin or a salt thereof. The formulation has a pharmaceutically acceptable solvent present in a rifabutin to solvent ratio of 4:1 to about 1:4, about 2:1 to about 1:3, or about 1:1 to about 1:2 w / v.

[0040] The bacterial infection may be any infection caused by A. baumannii, including, but not limited to, bacteremia, ventilator-associated bacterial pneumonia (VABP), hospital-acquired bacterial pneumonia (HABP), and urinary tract infection (UTI). Preferably, the bacterial species is A. baumannii.

[0041] Aspects of the present invention may also include an in vitro method for determining the susceptibility of a bacterial species to rifabutin. The method may include exposing a plurality of bacterial cells to an iron complex, an iron chelator, and rifabutin. The method may also include quantifying the number of the plurality of bacterial cells and / or identifying a decrease in the number of the bacterial cells. A decrease in the number of the bacterial cells indicates the susceptibility of the bacterial species to rifabutin. The method may also include administering rifabutin to a subject suffering from a bacterial infection of the bacterial species.

[0042] Other aspects and advantages of the present invention will become apparent from a consideration of the following detailed description thereof. [Brief explanation of the drawings]

[0043] [Figure 1] FIG. 1 is a graph illustrating the quantification of fhuE expression levels in A. baumannii HUMC1 in different media. [Figure 2] FIG. 2 is a graph of the activity of IV administered rifabutin in a murine neutropenic sepsis model. [Figure 3] Figure 3 shows the effect of rifabutin in a neutropenic pulmonary infection mouse model in CD-1 mice infected with A. baumannii UNT091. [Figure 4] Figure 4 shows the effect of rifabutin in a neutropenic pulmonary infection mouse model in CD-1 mice infected with A. baumannii UNT093. [Figure 5] Figure 5 shows the results of a dose fractionation experiment showing a clear dose-response relationship in which both Cmax and AUC are important for activity. [Figure 6] FIG. 6 is a graph showing CFU per lung pair in mice inoculated with A. baumannii. [Figure 7] FIG. 7 shows a schematic diagram of TonB-dependent transport. [Figure 8]FIG. 8 shows the activity of rifabutin and rifampin antibiotics upon plasmid-mediated expression of FhuE-variants in CA-MHB. DETAILED DESCRIPTION OF THE INVENTION

[0044] Detailed Description Embodiments of the present disclosure provide methods, uses, and compositions for treating A. baumannii infections or for making medicaments for treating A. baumannii infections. For background, see Howard, 2012, Acinetobacter baumannii. An emerging opportunistic See, for example, J. Bacteriol. Pathogen, Virulence 3(3):243-250 and Peleg, 2008, Acinetobacter baumannii. Emergence of a successful pathogen, Clin Microbiol Rev 21(3):538-582 (both incorporated by reference). The disclosed methods and compositions function through activation of the ferric-coprogen (FhuE) receptor to promote the entry of the rifabutin into the A. baumannii cells. The FhuE receptor is discussed in Sauer, 1987, Ferric-coprogen receptor FhuE of Escherichia coli. Processing and sequence common to all TonB-dependent outer membrane receptor proteins, J. Bacteriol. 169(5):2044-2049 (incorporated by reference).

[0045] The method preferably includes the steps of obtaining a sample from a patient suspected of having an infection; testing the sample to identify an A. baumannii infection in the patient; and determining the resulting AUC and C when administered to the patient to treat the patient. maxThe method may include providing a formulation of rifabutin that maximizes efficacy. The method may include administering the rifabutin formulation to the patient. Preferably, the formulation comprises rifabutin, water, a solvent, and an acid. Preferred solvents include polyoxyethylene sorbitan monooleate (Tween® 80), polyoxyethylene sorbitan monolaurate (Tween® 20), polyethylene glycol (PEG), propylene glycol, N-methyl-2-pyrrolidone (NMP), glycerin, ethanol, dimethylacetamide (DMA), diethylene glycol monoethyl ether (transcutol HP), dimethyl isosorbide (DMI), or another polar solvent. The formulation may be about 250 mg / ml (1:1 v / v solvent / water) or about 166.7 mg / ml (2:1 solvent / water), although the concentration of the reconstituted solution may be as high as about 300 mg / ml. In certain embodiments, the formulation is delivered to the patient, for example, by intravenous injection. Preferably, the IV injection contains a C of greater than about 2 mg / L, and optionally less than about 50 mg / L. max In some embodiments, the formulation comprises max The formulations include doses of rifabutin having an AUC of >2 mg / L but <50 mg / L, and >10 mg*h / L and <300 mg*h / L. The formulations can be delivered at doses of at least about 2 mg / kg q24h, 1 mg / kg q12h, or 0.5 mg / kg q6h. Referring to Figure 5, the formulations are preferably delivered via IV at doses of at least about 2 mg / kg q24h, 1 mg / kg q12h, or 0.5 mg / kg q6h.

[0046] The methods and compositions of the present disclosure take advantage of the insight that the A. baumannii siderophore receptor FhuE plays an important role in rifabutin uptake.

[0047] Figure 1 shows that fhuE is overexpressed at least 10-fold when A. baumannii is grown in nutrient-depleted medium (Roswell Park Memorial Institute (RPMI) medium + 10% fetal calf serum (FCS)) compared to standard test conditions (cation-adjusted Mueller Hinton broth; CA-MHB). As shown in the Examples, deletion of fhuE resulted in elevated MICs for rifabutin in RPMI + 10% FCS but, surprisingly, had no effect on the closely related compound rifampicin. These results confirm that FhuE is required for potent rifabutin activity in RPMI + 10% FCS and indicate that rifabutin activity in this medium is likely due to active uptake of the compound mediated by the A. baumannii siderophore receptor FhuE.

[0048] Figure 2 is a graph illustrating the results of the effects of rifabutin and rifampin in a neutropenic septic mouse model. The results show that IV administration of rifabutin protects against sepsis with a dose-dependent response at 1 mg / kg, whereas rifampin does not protect at 10 mg / kg, confirming the potent activity of rifabutin observed in vitro.

[0049] Figure 3 shows the effect of rifabutin in a neutropenic pulmonary infection mouse model in CD-1 mice infected with A. baumannii UNT091.

[0050] Figure 4 shows the effect of rifabutin in a neutropenic pulmonary infection mouse model in CD-1 mice infected with A. baumannii UNT093.

[0051] Figure 5 shows the C max We provide the results of a dose-fractionation experiment showing a clear dose-response relationship in which both AUC and AUC are important for activity.

[0052] In a preferred embodiment, the present disclosure provides a method for determining AUC and C max The present invention provides a method for treating A. baumannii infection by administering rifabutin in an amount that maximizes localized high C max and AUC, if required, can be achieved by intravenous injection or by inhalation by methods known in the art for modified oral release.

[0053] In certain embodiments, rifabutin has an AUC and C max In this manner, rifabutin reaches therapeutic concentrations and reduces the incidence of resistance. For example, in a preferred embodiment, max is greater than about 2 mg / L and less than about 50 mg / L.

[0054] Embodiments of the present disclosure provide a composition comprising rifabutin. In certain aspects, the present disclosure provides a composition for use in treating A. baumannii infection, the composition comprising rifabutin, water, a solvent, and an acid. The solvent can be polyoxyethylene sorbitan monooleate (Tween® 80), polyoxyethylene sorbitan monolaurate (Tween® 20), polyethylene glycol (PEG), propylene glycol, N-methyl-2-pyrrolidone (NMP), glycerin, ethanol, dimethylacetamide (DMA), diethylene glycol monoethyl ether (transcutol HP), or dimethyl isosorbide (DMI). The composition can comprise between about 1:1 and 2:1 v / v solvent / water. Most preferably, the composition is provided in an IV bag. In a preferred embodiment, the composition is provided for a patient identified as infected with A. baumannii, the composition comprising rifabutin for IV delivery at a dose of at least about 2 mg / kg q24h, 1 mg / kg q12h, or 0.5 mg / kg q6h. The composition contains a C of >2 mg / L but <50 mg / L. maxIt may have a formulation that provides a dose of rifabutin having an AUC of > 10 mg*h / L and < 300 mg*h / L.

[0055] Preferably, the formulation is intended for intravenous delivery.

[0056] In another aspect, the disclosure is the use of rifabutin for the manufacture of a medicament for treating an A. baumannii infection in a patient, wherein the medicament is formulated to be administered to the patient at a dosing regimen that results in a C max of at least about 2 mg / L. Preferably, the medicament comprises rifabutin, water, an acid, and a solvent (e.g., polyoxyethylene sorbitan monooleate (Tween® 80), polyoxyethylene sorbitan monolaurate (Tween® 20), polyethylene glycol (PEG), propylene glycol, N-methyl-2-pyrrolidone (NMP), glycerin, ethanol, dimethylacetamide (DMA), diethylene glycol monoethyl ether (transcutol HP), or dimethyl isosorbide). In a preferred embodiment, the solvent is DMI or transcutol HP. In certain embodiments, the solvent to water ratio v / v is 1:1 or 1:2. The acid can be hydrochloric acid, methanesulfonic acid, phosphoric acid, L-tartaric acid, D-glucuronic acid, L-malic acid D-gluconic acid, L-lactic acid, acetic acid, or L-aspartic acid. In a preferred embodiment, the acid is acetic acid or D-glucuronic acid. In certain embodiments, the molar ratio of rifabutin to acid is 1:1.

[0057] Most preferably, the medicament is provided in an IV bag. In a preferred embodiment of use, the dosing regimen results in 2 mg / L < C max < 50 mg / L; and 10 mg*h / L < AUC < 300 mg*h / L. The dosing regimen can preferably result in a dose of at least about 2 mg / kg q24h, 1 mg / kg q12h, or 0.5 mg / kg q6h.

[0058] If necessary, the rifabutin is administered in a dose-dependent manner. max Such methods and compositions allow rifabutin to reach therapeutic concentrations and reduce the incidence of resistance development.

[0059] In some embodiments, rifabutin is C max and AUC, and AUC and C max t so as to maximize max To minimize side effects, rifabutin may be administered via a modified release oral drug delivery system. Such systems and methods allow rifabutin to reach therapeutic concentrations and reduce the incidence of resistance development. [Example]

[0060] Example 1 Many approved drugs were tested against A. baumannii under standard test conditions (cation-adjusted Mueller Hinton broth; CA-MHB) and nutrient-poor medium (Roswell Park Memorial Institute (RPMI) medium + 10% fetal calf serum (FCS)). The antibacterial activity of rifabutin against A. baumannii was greatly enhanced under nonstandard test conditions. Table 1 summarizes the antimicrobial susceptibility results of the carbapenem-resistant A. baumannii strains HUMC1 and UNT091 under standard (CA-MHB, Mueller Hinton broth 2) and nonstandard test conditions. The results above show that two carbapenem-resistant A. baumannii strains, HUMC1 and UNT091, were highly susceptible to rifabutin (MIC = 0.002 mg / L) when tested in RPMI supplemented with 10% FCS, but exhibited low susceptibility to rifampin, meropenem, cefotaxime, gentamicin, and ciprofloxacin. In striking contrast, both strains had low susceptibility to all of the antibiotics tested (including rifabutin) when tested under standard test conditions (CA-MHB broth).

[0061] [Table 1]

[0062] Methods for testing in Example 1, Table 1. The in vitro activities of rifabutin, rifampin, meropenem, cefotaxime, gentamicin, and ciprofloxacin against two carbapenem-resistant clinical A. baumannii isolates in Roswell Park Memorial Institute (RPMI) medium supplemented with 10% (v / v) fetal calf serum (FCS) and under standard minimum inhibitory concentration (MIC) assay conditions were analyzed.

[0063] Rifabutin stock solution was prepared at 2 mg / mL in DMSO and stored at -20°C.

[0064] Two A. baumannii isolates were used in this example: HUMC1 (BV374) (Spellberg / Luna Laboratory, University of Southern California, Los Angeles, CA) and UNT091-1 (BV378) (UNT Health Science Center, Fort Worth, TX). The HUMC1 isolate is a highly pathogenic, drug-resistant clinical strain isolated from a bloodstream infection. Both strains are carbapenem-resistant and colistin-susceptible. The isolates were stored as 20% (v / v) glycerol cultures at -80°C.

[0065] MICs were determined by the broth microdilution method according to Clinical Laboratory Standards Institute (CLSI) guidelines, using RPMI supplemented with 10% (v / v) or cation-adjusted Muller Hinton broth (CA-MHB) as the assay medium. To prepare the bacterial inoculum, 3–5 colonies of the bacterial strain from overnight growth on a ChromAgar orientation plate (CHROMagar catalog number RT412) were suspended in 5 mL of saline. The turbidity of the bacterial suspension was adjusted to 0.5 McFarland units (optical density at 610 nm (OD610) equals 0.08–0.1). This suspension was diluted 200-fold in RPMI supplemented with 10% (v / v) FCS to reach a final concentration of approximately 106 colony-forming units (CFU) / mL and used to inoculate microtiter plates.

[0066] Serial two-fold dilutions of the above antibiotics were prepared in separate 96-well polypropylene U-bottom plates (Ratiolab catalog number 6018111) in RPMI supplemented with 10% (v / v) FCS at 10x the final test concentrations, and 10 ml of the dilutions were transferred to a new 96-well polystyrene U-bottom microtiter plate with a parafilm plate cover.

[0067] The plates were then inoculated with 90 μL / well of the prepared bacterial suspension using a multichannel pipette (Eppendorf), including 4 wells in the first column (each growth control (no antibiotic)). The plates were covered with parafilm and incubated at 35°C for 20-24 hours, after which MICs were determined by visual inspection, the plates were scanned, and the data recorded. The MIC was recorded as the lowest concentration of compound that inhibited bacterial growth by visual inspection. MICs were determined at least in duplicate, and in case of variation, the higher value is provided.

[0068] Example 2. FhuE overexpression: The level of ftiuE expression was assessed in different media by qRT-PCR against A. baumannii strain HUMC1.

[0069] Figure 1 shows a graph illustrating the quantification of fhuE expression levels in different media. As shown, fhuE is overexpressed approximately 10-fold when A. baumannii is grown in RPMI + 10% FCS or CA-MHB supplemented with 0.1 mM pyridoxal isonicotinoyl hydrazone (PIH) compared to CA-MHB. These results indicate that the increased rifabutin activity is due to increased fhuE expression in these media.

[0070] Method for measuring fhuE expression levels. Figure 1. Expression of fhuE was assessed by quantitative reverse transcription-PCR (qRT-PCR). Isolates were grown in specific broth at 37°C to mid-logarithmic phase (optical density at 600 nm [OD600] 0.5), and total RNA was extracted using the PureLink RNA Mini Kit (Ambion) according to the manufacturer's recommendations. Residual DNA contamination was removed using the Turbo DNA-free kit (Ambion). qRT-PCR was performed using the GoTaq 1-Step RT-qPCR System kit (Promega) on a CFX96 Touchscreen. TM The PCR was performed using a Real-Time PCR Detection System (BioRad). RNA polymerase sigma factor D (rpoD) was quantified as a housekeeping gene, and fhuE expression was normalized to that of rpoD using the comparable ΔΔC (where C is the threshold cycle) method.

[0071] Example 3. Deletion of fhuE To confirm the role of FhuE activation in rifabutin activity, fhuE was deleted in A. baumannii strains HUMC1 and UNT091.

[0072] Table 2 summarizes the MICs of rifabutin in RPMI medium supplemented with 10% (v / v) FCS for the fhuE deletion strains and their parent strains. This resulted in elevated MICs for rifabutin in RPMI + 10% FCS, but surprisingly had no effect on the closely related compound, rifampicin. These results confirmed that FhuE is required for potent rifabutin activity in RPMI + 10% FCS and indicated that rifabutin activity in this medium is likely due to active uptake of the compound mediated by the A. baumannii siderophore receptor FhuE. Data from this experiment indicate that rifabutin is highly active against A. baumannii due to a novel entry mechanism in A. baumannii.

[0073] [Table 2]

[0074] Table 2. Method for constructing fhuE deletion mutants. The gene encoding the FhuE protein, AWC45_RS10145 (HUMC1 genome), was deleted in A. baumannii strains HUMC1 and UNT091 using a two-step recombination method. DNA fragments corresponding to 700 bp upstream and downstream genomic regions of fhuE were amplified by PCR and introduced into the pVT77 knockout plasmid using Gibson assembly. The resulting fhuE knockout plasmid was transferred to A. baumannii isolates by conjugation, and trans-conjugates were selected on LB agar plates containing sodium tellurite. After overnight selection at 37°C, clones were screened for genomic plasmid integration by PCR, and clones containing upstream and downstream plasmid integrations were used for counter-selection on LB agar plates containing AZT for plasmid removal from the genome. Clones were screened for fhuE deletion and plasmid removal by PCR, and the genomic gene deletion was confirmed by DNA sequencing (Microsynth AG, Balgach, Switzerland).

[0075] Example 4. Plasmid-based expression of fhuE: Overexpression of fhuE was evaluated to determine whether it induces rifabutin uptake. Table 3 summarizes the MICs of rifabutin in fhuE-expressing A. baumannii strains in CA-MHB + / - 1 mM IPTG. In the presence of IPTG, the rifabutin MIC was 1000-fold lower in the strain harboring the fhuE-expressing plasmid compared to the strain harboring the empty plasmid as a control. This data indicates that activation of fhuE in A. baumannii results in potent activity of rifabutin against this organism.

[0076] [Table 3]

[0077] Methods for overexpression of fhuE in A. baumannii, Table 3 The fhuE gene from A. baumannii strain HUMC1 (AWC45 RS10145) was cloned into the E. coli / A. baumannii shuttle plasmid pVT111 under the control of the isopropyl-β-D-1-thiogalactopyranoside (IPTG)-inducible promoter Ptrc-lacO. The resulting plasmid and the original pVT111 plasmid (control) were transferred into A. baumannii strain ATCC-17978 by conjugation, and transconjugates were selected on LB agar plates containing kanamycin. The presence of the plasmid in the recipient A. baumannii strain was then confirmed by PCR.

[0078] Example 5: Frequency of Mutational Resistance (FoR) to Rifabutin Table 4 summarizes the FoR results of the frequency of spontaneous resistance of A. baumannii to rifabutin on RPMI + 10% FCS agar medium. -5 ~10 -9 A dose-dependent FoR ranging from 10 to 100 was observed for the HUMC1 strain. -5 High FoR per 100 mg / L was observed at rifabutin concentrations of 0.02 mg / L and 0.2 mg / L, followed by 10 mg / L at 1 mg / L. -7 , and 10 mg / L and 20 mg / L rifabutin -9 A gradual decrease to was observed. Similar results were observed for strains UNT091-1, ACC00445, LAC-4 and UNT238-1.

[0079] [Table 4]

[0080] Five clinical A. baumannii strains were resistant to rifabutin at concentrations >2 mg / L. -9 reveals a dose-dependent frequency of resistance mutations reaching a similar in vitro FoR (10 -9) was also shown for other antibiotics used as standard of care to treat A. baumannii infections. The results indicate that rifabutin can be used to effectively treat A. baumannii infections. Importantly, it was determined that the route of administration must achieve a systemic drug concentration of >2 mg / L (a concentration not achievable with currently available oral formulations) to prevent rapid resistance development.

[0081] Methods for determining the frequency of mutational resistance to rifabutin, Table 4. The frequency of A. baumannii mutant resistance (FoR) to rifabutin in RPMI medium supplemented with 10% (v / v) fetal calf serum (FCS) was investigated.

[0082] A stock solution of rifabutin was prepared at 10 mg / mL in DMSO and stored at −20° C. A. baumannii clinical isolate was stored at −80° C. as 20% (v / v) in glycerol stock cultures.

[0083] Selective agar plates were prepared using RPMI powder (Sigma R7755) dissolved at 10.3 g / L with 15 g / L agar and boiled until the agar was completely dissolved. After cooling the medium to 45°C, 0.3 g / L L-glutamine (Sigma G7513), 25 mM HEPES (Gibco 15630-056), and 10% (v / v) FCS (Gibco 10500-064) were added. Rifabutin concentrations of 0.02 mg / L, 0.1 mg / L, 1.0 mg / L, 2.0 mg / L, and 20.0 mg / L were added, and 25 mL of the medium was poured directly into 9 cm Petri dishes.

[0084] The culture inoculum was approximately 5 x 10 5A bacterial NaCl suspension was prepared in 0.5 McFarland® solution, diluted 200-fold in 100 mL of RPMI (Sigma R8758) + 10% FCS in a 500 mL flask to reach CFU / mL. The flask was incubated for 24 hours at 37°C with shaking at 220 rpm. After incubation, the cells were pelleted by centrifugation (10 minutes at RT at 7000 rpm) and resuspended in 1 mL of PBS. Ten-fold serial dilutions of the cell suspension were prepared in PBS, and 100 μL of the resulting cell suspension was inoculated onto rifabutin-containing selective plates and non-selective plates to determine the cell density of the inoculum. After 24 hours of incubation at 35°C, colonies formed, and the frequency of resistance was calculated as the ratio between the number of colonies growing on the antibiotic-containing plates and the total colony count of the inoculum.

[0085] Example 6: In vitro testing Figure 2 is a graph illustrating the results of the effects of rifabutin and rifampin in a neutropenic septic mouse model (n=7). The CD-1 mice were infected IP with A. baumannii ACC00445 strain in the presence of 5% mucin. The mice were treated with rifabutin and rifampin via IV administration at 1 and 5 hours post-infection. The results show that IV administration of rifabutin protects against sepsis in a dose-dependent manner at 1 mg / kg, whereas rifampin does not protect at 10 mg / kg. This confirms the potent activity of rifabutin observed in vitro.

[0086] Figure 3 is a graph illustrating the results of the effect of rifabutin in a neutropenic pulmonary infection mouse model in which CD-1 mice were intranasally infected with A. baumannii UNT091 (n=5 / dose group). The mice were treated with rifabutin via IV administration 2 hours post-infection.

[0087] Figure 4 is a graph illustrating the effects of rifabutin in a neutropenic pulmonary infection mouse model (n=5 / dose group) in which CD-1 mice were intranasally infected with A. baumannii UNT093. The mice were treated with rifabutin via IV administration 2 hours post-infection.

[0088] Twenty-four hours after treatment, the mice were sacrificed and colony-forming units in the lungs were measured. The results show that IV administration of rifabutin produces potent effects at doses of <0.5 mg / kg, confirming the potent activity of rifabutin observed in vitro.

[0089] Figure 5 summarizes the results of a dose-fractionation study in a neutropenic mouse model of infection. Rifabutin was administered IV either once daily (q24h), twice daily (q12h), or four times within a 24-hour period (q6h). The results show a clear dose-response relationship in which both Cmax and AUC are important for activity.

[0090] Table 5 shows the target exposure required to treat A. baumannii infection based on MIC. Estimates are based on an efficacy model, a sigmoidal Eq. with a slope of the variables to fit the dose and PK / PD index (PDI) response. max The model was used in GraphPad Prism version 5.03 (GraphPad, Inc., San A rifabutin PDI value that produces a 1-log reduction in lung CFU was determined using a rifabutin ELISA kit (Dietary, CA). This data demonstrates that oral administration of rifabutin does not achieve the exposure required to treat >90% of A. baumannii isolates (MIC <1 mg / L).

[0091] [Table 5]

[0092] The above in vivo studies demonstrate that IV administration of rifabutin is as potent and effective in vivo as it is in vitro. Thus, the unexpected finding that rifabutin exhibits potent activity against A. baumannii under nutrient-limited conditions (particularly iron-limited conditions) due to activation via the fhuE siderophore transporter and uptake into bacterial cells allows for potent activity in mouse models of infection. In particular, IV rifabutin formulations are effective against A. baumannii infection.

[0093] Figure 6 is a graph showing CFU per lung pair in mice inoculated with A. baumannii strains. Neutropenic female CD-1 mice (5 per group) were inoculated with A. baumannii strains at equal titers (6.90 and 6.93 log 10 Mice were inoculated intranasally (t = 0 h) with 100 CFU (1000 CFU) of A. baumannii UNT091-1 wild-type and A. baumannii UNT091-1 ΔfhuE mutant. Treatment (single IV dose) was administered 2 h postinfection, and bacterial burden was reported at 26 h by determining CFU / lung. Furthermore, the effect of RBT was blunted in mice infected with the UNT091-1::ΔfhuE strain. This confirmed the role of fhuE in mediating RBT susceptibility both in vitro and in vivo.

[0094] Example 7: The in vitro activity of rifabutin was determined against a panel of clinical A. baumannii in the presence of iron chelators, which results in increased siderophore receptor expression. Rifabutin exhibits potent in vitro activity against a large panel of recently isolated, primarily XDR A. baumannii strains, including isolates that are nonsusceptible to colistin and carbapenems. Complexation of free iron by PIH allows robust rifabutin susceptibility testing in nutrient-rich standard MHA.

[0095] All isolates were resistant to carbapenems. Rifabutin showed excellent activity against A. baumannii in iron-chelated, nutrient-rich MHA with an MIC50 / MIC90 of 0.008 / 1 mg / L, comparable to liquid MIC determinations using RPMI supplemented with FCS (MIC50 / MIC90 of 0.004 / 2 mg / L). In contrast, standard MHA rifabutin had negligible activity.

[0096] Methods for determining in vitro activity A panel of 293 CRAB strains isolated between 2017 and 2019 from Europe (n = 144), the United States (USA) (n = 99), and the Asia-West Pacific (n = 50) regions was used for rifabutin MIC determination. The panel of strains included isolates with 10% MDR (n = 29), 86% XDR (n = 253), and 4% PDR (n = 11) phenotypes. Isolates were primarily collected from patients with pneumonia (59%), bloodstream infections (28%), and skin and soft tissue infections (11%) and belonged to the antimicrobial class described by Magiorakos et al. (2011). < If non-susceptible according to CLSI breakpoints 2, they were classified as XDR according to CLSI breakpoints. Susceptibility testing of A. baumannii to rifabutin was performed using the agar dilution method on Muller Hinton Agar (MHA) supplemented with 0.1 mM pyridoxal isonicotinoyl hydrazone (PIH), a potent, non-toxic iron chelator. Comparator antibiotics were tested under CLSI standard conditions.

[0097] Example 8: Modeling the effect of FhuE TonB on rifabutin activity In complementation assays, FhuE V38P expression failed to restore the potent activity of rifabutin compared with wild-type FhuE expression. This indicates that a physical interaction between the FhuE TonB box and the TonB energy transducing machinery is required for the potent activity of rifabutin, as shown in Figure 8. These data suggest that rifabutin binding to FhuE is required to activate the FhuE allosteric conformational transition, which enables active transport of rifabutin and potent activity against A. baumannii. Figure 8 shows the activity of rifabutin and rifampicin antibiotics upon plasmid-mediated expression of FhuE variants in CA-MHB. A. baumannii ATCC-17978 was used as the host strain. Gene expression from the plasmid was induced with 1 mM IPTG; a plasmid not encoding fhuE was used as a control.

[0098] Methods for determining the effect of TonB on rifabutin activity The potent activity of rifabutin against A. baumannii depends on the expression of the TonB-dependent transporter (TBDT) FhuE. This suggests that rifabutin is actively translocated across the A. baumannii outer membrane via FhuE. TBDT-mediated active transport requires specific substrate binding to activate an allosteric conformational transition of the transporter, which results in recruitment of the TonB energy transduction mechanism via the so-called TonB box of TBDT, as shown in Figure 7. See Noinaj, N., Guillier, M., Barnard, TJ & Buchanan, SK, TonB-dependent transporters: regulation, structure, and function. Annu. Rev. Microbiol. 64, 43-60 (2010) (incorporated herein by reference). Figure 7 is a compilation of data from Hickman, SJ, Cooper, REM, Bellucci, L., Paci, E. & Brockwell, D.J. Gating of TonB-dependent transporters by substrate-specific forced remodeling. Nat. Commun. 8, 1-12 (2017) (incorporated herein by reference). TBDTs are so-called gated porins whose lumen is blocked by an N-terminal plug domain, preventing substrate passage across the outer membrane. Substrate binding induces allosteric rearrangement of the plug domain, releasing the Ton box into the periplasmic space, where it recruits the C-terminal domain of TonB in a complex with ExbB and ExbD to form the energy transduction mechanism. Linkage of the OM and IM via this noncovalent complex is required to trigger complete or partial unfolding of the plug domain, allowing the substrate to pass through. TBDT: TonB-dependent transporter, OM: outer membrane, IM: inner membrane, PG: peptidoglycan.

[0099] To investigate whether rifabutin is actively transported, we generated the FhuE V38P mutant, which has a mutation in the TonB box that disrupts the interaction between FhuE and TonB. Cadieux, N., Bradbeer, C. & Kadner, RJ. Sequence changes in the ton box region of BtuB affect its transport activities and interaction with TonB protein. J. Bacteriol. 182, 5954-5961(2000); Funahashi, T. et al. Identification and characterization of an outer membrane receptor gene required in Acinetobacter baumannii. for utilization of desferricoprogen, rhodotorulic acid, and desferrioxamine B as xenosiderophores. Biol. Pharm. Bull. 35, 753-760(2012); the contents of each of which are incorporated herein by reference.

[0100] Incorporation by Reference References and citations to other documents (e.g., patents, patent applications, patent publications, journals, books, articles, web content) are made throughout this disclosure. All such documents are incorporated herein by reference in their entirety for all purposes.

[0101] equivalent Various modifications of the invention and many further embodiments thereof, in addition to those shown and described herein, will become apparent to those skilled in the art from the entire contents of this document, including reference to the scientific and patent literature cited herein. The subject matter herein contains important information, exemplification, and guidance that can be adapted to the practice of this invention in its various embodiments and equivalents thereof.

Claims

[Claim 1] The invention described in this specification.

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